crossing96/oncoscreening huggingface dataset:
Tumor immune microenvironment and clinical outcomes in stage IV urothelial cancer: YODO study.	BACKGROUND: Bladder cancer is the 10th most common cancer globally, with a growing incidence in Japan. Evaluation of molecular, genetic, and cellular biomarkers that predict treatment response and prognosis in patients with metastatic urothelial carcinoma (mUC) may help optimize sequential treatment strategies with chemotherapy and immune checkpoint inhibitors (ICIs). METHODS: This multicenter, retrospective cohort study, evaluated programmed death-ligand 1 (PD-L1) expression, tumor mutational burden (TMB), and cancer-immune phenotype as predictive prognostic biomarkers following first-/second-line treatment in Japanese adult patients with mUC. The primary endpoint was prevalence of PD-L1 expression. Secondary endpoints were TMB, overall survival (OS), and progression-free survival (PFS) from initiation of first-line treatment, and exploratory endpoints were cancer-immune phenotype, OS, PFS, and treatment response according to potential biomarker status. RESULTS: Of the 143 patients included (mean age 71.7 years), PD-L1 expression was high in 29.4% of patients. Non-synonymous TMB was high in 33.6% and low in 66.4%. Cancer-immune phenotype was immune-desert in 62.9%, immune-excluded in 30.8%, and inflamed in 6.3%. Median OS and PFS following first-line treatment were 18.2 and 7.4 months, respectively. Overall response to second-line treatment was slightly better with high versus low/negative PD-L1 expression. PD-L1 expression and TMB were non-significant predictors of OS or PFS, whereas immune-excluded phenotype was associated with better OS in comparison with immune-desert phenotype. CONCLUSION: PD-L1 expression and TMB were non-significant predictors of prognosis after first-line treatment in Japanese patients with mUC, but cancer-immune phenotype may be an important prognostic factor in chemotherapy-ICI sequential treatment strategies. Clinical trial registration number UMIN000037727.	bladder
Circular RNA_0000326 accelerates breast cancer development via modulation of the miR-9-3p/YAP1 axis.	Circular RNA (circ)_0000326 has been reported in bladder cancer and cervical cancer and is concerned to be involved with the development of cancerous cells. Whereas, there have been no reports concentrating on the influences of circ_0000326 in breast cancer (BC). Therefore, the latent modulatory mechanisms of circ_0000326 in BC are researched. circ_0000326 expression in BC tissues and correlative cells was evaluated via RT-qPCR, and the relevance between circ_0000326 expression and overall survival and the clinicopathological feature was also investigated. After a series of transfection, the effects of circ_0000326, microRNA-9-3p (miR-9-3p), and Yes-associated protein 1 (YAP1) in BC cell growth, invasion, and stemness were studied by CCK-8, flow cytometry, Transwell, and sphere-forming assays. The binding sites and correlation of circ_0000326, miR-9-3p, and YAP1 were certified via starBase website, luciferase reporter assay, and Pearson's χ2 test. The in vivo experiment was evaluated by establishing a subcutaneous tumorigenesis model. High-expressed circ_0000326 in BC tissues and cells was discovered, which was connected with an undesirable prognosis. Silencing of circ_0000326 visibly inhibited MCF-7 and BT549 cell growth, invasion, stemness, meanwhile declining the protein levels of SRY-related high-mobility group box gene 2 (SOX2) and octamer binding transcription factor 4 (OCT4). miR-9-3p was a sponger of circ_0000326, which was negatively regulated by circ_0000326. Moreover, YAP1 was confirmed as a target gene of miR-9-3p. circ_0000326 affected BC cell behaviors via mediating miR-9-3p and YAP1. Furthermore, circ_0000326 silencing prohibited tumor growth of BC in vivo. The research uncovered that circ_0000326 facilitated BC development via mediating the miR-9-3p/YAP1 axis.	bladder
Evaluation of sarcopenia in patients receiving intravesical Bacillus Calmette-Guérin for non-muscle invasive bladder cancer.	BACKGROUND: Sarcopenia is associated with adverse outcomes for patients with muscle invasive bladder cancer (MIBC), but less is known about its impact in the setting of non-muscle invasive bladder cancer (NMIBC). Sarcopenia, skeletal muscle density, and adipose tissue area have been studied as markers of malnutrition and can be determined radiographically. The purpose of this study is to characterize the prevalence of sarcopenia in patients with NMIBC receiving intravesical Bacillus Calmette-Guérin (BCG). METHODS: Following institutional review board approval, patients with NMIBC having received intravesical BCG were identified using institutional pharmacy records. Patients having undergone computed tomography (CT) of the abdomen and pelvis within 90 days of treatment were included in the analysis. Using sliceOmatic 5.0 software, skeletal muscle area (cm(2)) was measured at the L3 level to calculate skeletal muscle index (SMI), a marker of sarcopenia. Subcutaneous, visceral, and intramuscular adipose tissue areas in addition to skeletal muscle density were also measured. Frailty was evaluated as a secondary aim using the 5-Item Modified Frailty Index (mFI-5). Using predefined cutoffs, the prevalence of sarcopenia was determined. Descriptive statistics were used to characterize frailty and secondary body composition characteristics. Statistical analysis was performed to evaluate the impact of sarcopenia on recurrence rate and progression. RESULTS: A total of 308 patients having received BCG between 2015 and 2020 were identified, of which 90 met criteria for analysis. Nearly all (94%) patients completed at least 5 out of 6 BCG induction instillations. Median body mass index (kg/m(2)) was 27.64 (IQR 24.9, 30.5) for females and 27.7 (IQR 24.9, 30.66) for males. Median SMI (cm(2)/m(2)) was 49.44 (IQR 39.39, 55.17) for females and 49.58 (IQR 40.25, 55.58) for males. A majority (61%) of patients were found to be sarcopenic. High-risk frailty was identified 36% of patients. There was no association between sarcopenia and recurrence rate or progression. CONCLUSIONS: Sarcopenia and frailty are highly prevalent amongst patients with NMIBC. A diagnosis of NMIBC represents a window of opportunity to identify and intervene on modifiable risk factors such as sarcopenia and frailty, which are associated with adverse outcomes in more advanced disease states.	bladder
Classification of formalin-fixed bladder cancer cells with laser tweezer Raman spectroscopy.	Bladder cancer is a common cancer that is relatively hard to detect at an early stage because of its non-obvious symptoms. It is known that bladder cells can be found in urine samples which potentially could be used for early detection of bladder cancer. Raman spectroscopy is a powerful non-invasive tool for accessing biochemical information of cells. Combined with laser tweezers, to allow isolation of single cells, Raman spectroscopy has been used to characterise a number of bladder cells that might be found in a urine sample. Using principal component-canonical variates analysis (PC-CVA) and k-fold validation, the results shows that the invasive bladder cancer cells can be identified with accuracy greater than 87%. This demonstrates the potential of developing an early detection method that identifies the invasive bladder cancer cells in urine samples.	bladder
An HGF-dependent positive feedback loop between bladder cancer cells and fibroblasts mediates lymphangiogenesis and lymphatic metastasis.	BACKGROUND: Cancer-associated fibroblasts (CAFs) play a vital role in facilitating tumor progression through extensive reciprocal interplay with cancer cells. Tumor-derived extracellular vesicles (EVs) are the critical mediators involved in the crosstalk between cancer cells and stromal cells, contributing to the metastasis of cancers. Yet, the biological mechanisms of tumor-derived EVs in triggering CAFs phenotype to stimulate the lymph node (LN) metastasis of bladder cancer (BCa) are largely unknown. Here, we aimed to explore the effects and molecular mechanisms of tumor-derived EV-mediated CAFs phenotype in regulating BCa LN metastasis. METHODS: The high-throughput sequencing was utilized to identify the crucial long non-coding RNA (lncRNA) associated with CAF enrichment in BCa. The functional role of the transition of fibroblasts to CAFs induced by LINC00665-mediated EVs was investigated through the in vitro and in vivo assays. Chromatin isolation by RNA purification assays, fluorescence resonance energy transfer assays, cytokine profiling and patient-derived xenograft (PDX) model were performed to explore the underlying mechanism of LINC00665 in the LN metastasis of BCa. RESULTS: We found that CAFs are widely enriched in the tumor microenvironment of BCa, which correlated with BCa lymphangiogenesis and LN metastasis. We then identified a CAF-associated long non-coding RNA, LINC00665, which acted as a crucial mediator of CAF infiltration in BCa. Clinically, LINC00665 was associated with LN metastasis and poor prognosis in patients with BCa. Mechanistically, LINC00665 transcriptionally upregulated RAB27B expression and induced H3K4me3 modification on the promoter of RAB27B through the recruitment of hnRNPL. Moreover, RAB27B-induced EVs secretion endowed fibroblasts with the CAF phenotype, which reciprocally induced LINC00665 overexpression to form a RAB27B-HGF-c-Myc positive feedback loop, enhancing the lymphangiogenesis and LN metastasis of BCa. Importantly, we demonstrated that blocking EV-transmitted LINC00665 or HGF broke this loop and impaired BCa lymphangiogenesis in a PDX model. CONCLUSION: Our study uncovers a precise mechanism that LINC00665 sustains BCa LN metastasis by inducing a RAB27B-HGF-c-Myc positive feedback loop between BCa cells and fibroblasts, suggesting that LINC00665 could be a promising therapeutic target for patients with LN metastatic BCa.	bladder
Comparison of holmium laser, bipolar and conventional monopolar transurethral resection of bladder tumour in primary non-muscle invasive bladder cancer.	OBJECTIVES: To compare the efficiency and safety profile of conventional monopolar, bipolar plasmakinetic and holmium laser techniques for transurethral resection of bladder tumour. METHOD: The prospective comparative study was conducted from July 2019 to May 2021 after approval from the ethicsreview committee of Kafrelsheikh University, Egypt, and comprised patients of either gender with primary non muscle invasive bladder cancer who qualified for transurethral resection of bladder tumour. The patients were stratified into low-risk group A, intermediate risk group B and high-risk group C in accordance with the guidelines of the European Association of Urology. Comprehensive cystoscopy and panendoscopy were done in all cases. Once panendoscopy was done, tumour resection was performed with monopolar resectoscope in group A, plasmakinetic resectoscope in group B and holmium laser in group C). Data was collected at preoperative, peroperative, postoperative and follow-up stages. Data was analysed using SPSS 21. RESULTS: Of the 84 patients, 67(79.76%) were males and 17(20.23%) were females. There were 27(32.14%) patients in group A; 21(77.8%) males and 6(22.2%) females withy mean age 60.63±11.76 years. Group B had 32(38%) patients; 26(81.2%) males and 6(18.8%) females with mean age 65.34±7.55 years. Group C had 25(29.76%) patients; 20(80%) males and 5(20%) females with mean age 59.48±12.6 years. The mean follow-up period was 12.97±2.70 months in group A, 12.81±2.75 monthsin group B and 13.48±3.3 monthsin group C. Visualised complete resection was done in 23(85.8%) group A patients, 29(90.6%) group B patients and 24(96%) group C patients(p=0.018). Visualised complete resection, tumour multiplicity, tumour size, catheter duration, and hospital stay were significant predictors (p<0.05). Survival analysis showed 26(96.3%), 30(93.75%) and 25(100%) cases in groups A, B and C, respectively. CONCLUSIONS: Bipolar plasmakinetic and holmium laser techniques were found to be more effective and safer than the conventional monopolar technique for transurethral resection of bladder tumour in patients with primary non-muscle invasive bladder cancer.	bladder
Racial and sex differences in tumor genomics in urothelial carcinoma.	PURPOSE: Differences in bladder cancer outcomes have been demonstrated by sex and race/ethnicity, with studies showing a higher burden of adverse outcomes among women and racially minoritized populations. Despite these epidemiologic differences, populations with disproportionally adverse outcomes are often underrepresented in genomic cohorts. This exclusion impacts the accuracy and generalizability of genomic studies in bladder cancer and has the potential to widen disparities by sex and/or race/ethnicity. BASIC PROCEDURES: We analyzed pooled somatic mutational data from publicly available cohorts in the cBioPortal open access platform. FINDINGS: A total of 796 unique patients were identified. Average age for the cohort was 67 years (range: 25-98 years), 188 (24%) were female, and the majority were White (n = 423, 85% among those who report race). Median total mutation count was 91 (IQR: 20, 202) per patient. We used multivariable logistic regression to independently evaluate the association between race/sex and mutation status in each of 122 genes of interest, identified from TCGA, adjusting for age and bladder cancer invasive status. In adjusted analyses, male sex was associated with increased risk of mutation in ARID1A, CHD6, and NCOR1 compared with female sex. White race was associated with increased risk of mutation in ARID1A, EP300, PIK3CA, and TP53 and decreased risk of mutation in HRAS compared with non-White race. CONCLUSIONS: These differences highlight the importance of enriching cohorts for female and non-White patients in genomic studies and clinical trials, especially as we test the use of molecular biomarkers to personalize care for patients with bladder cancer.	bladder
LncRNA UCA1 could regulate the progression of neuropathic pain by regulating miR-135a-5p.	BACKGROUND: Neuropathic pain (NPP) is known as a common neurological disease with high incidence rate. The present work focused on the roles of long non-coding RNA urothelial carcinoma antigen 1(LncRNA UCA1) in NPP and the possible underlying mechanism. METHODS: NPP rat model has been established and the levels of UCA1 NPP as well as the group has been determined by RT-PCR method. Next, NPP rats were treated by UCA1 over-expression plasmid and the behaviors, as well as expression of inflammatory cytokines have been examined. Furthermore, target miRNA of UCA1, miR-135a-5p, has been predicted by bioinformatic method, and further verified with the dual-luciferase reporter assay. Finally, the effects of UCA1/ miR-135a-5p axis have been further evaluated. RESULTS: Expressions of UCA1 were markedly decreased and miR-135a-5p were significantly increased in NPP rats in comparison with the control rats. Over-expression of UCA1 alleviated the inflammatory condition in NPP model by decreasing expression of inflammatory cytokines. miR-135a-5p was confirmed to be a target microRNA of UCA1, and UCA1 may regulate the progress of NPP via targeting miR-135a-5p. CONCLUSION: UCA1 could regulate NPP via affecting miR-135a-5p expression.	bladder
Comprehensive analysis of cuproptosis-related lncRNAs signature to predict prognosis in bladder urothelial carcinoma.	BACKGROUND: Cuproptosis-related genes (CRGs) have been recently discovered to regulate the occurrence and development of various tumors by controlling cuproptosis, a novel type of copper ion-dependent cell death. Although cuproptosis is mediated by lipoylated tricarboxylic acid cycle proteins, the relationship between cuproptosis-related long noncoding RNAs (crlncRNAs) in bladder urothelial carcinoma (BLCA) and clinical outcomes, tumor microenvironment (TME) modification, and immunotherapy remains unknown. In this paper, we tried to discover the importance of lncRNAs for BLCA. METHODS: The BLCA-related lncRNAs and clinical data were first obtained from The Cancer Genome Atlas (TCGA). CRGs were obtained through Coexpression, Cox regression and Lasso regression. Besides, a prognosis model was established for verification. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene ontology (GO) analysis, principal component analysis (PCA), half-maximal inhibitory concentration prediction (IC50), immune status and drug susceptibility analysis were carried out. RESULTS: We identified 277 crlncRNAs and 16 survival-related lncRNAs. According to the 8-crlncRNA risk model, patients could be divided into high-risk group and low-risk group. Progression-Free-Survival (PFS), independent prognostic analysis, concordance index (C-index), receiver operating characteristic (ROC) curve and nomogram all confirmed the excellent predictive capability of the 8-lncRNA risk model for BLCA. During gene mutation burden survival analysis, noticeable differences were observed in high- and low-risk patients. We also found that the two groups of patients might respond differently to immune targets and anti-tumor drugs. CONCLUSION: The nomogram with 8-lncRNA may help guide treatment of BLCA. More clinical studies are necessary to verify the nomogram.	bladder
A machine learning model based on MRI for the preoperative prediction of bladder cancer invasion depth.	OBJECTIVES: To construct and validate a prediction model based on full-sequence MRI for preoperatively evaluating the invasion depth of bladder cancer. METHODS: A total of 445 patients with bladder cancer were divided into a seven-to-three training set and test set for each group. The radiomic features of lesions were extracted automatically from the preoperative MRI images. Two feature selection methods were performed and compared, the key of which are the Least Absolute Shrinkage and Selection Operator (LASSO) and the Max Relevance Min Redundancy (mRMR). The classifier of the prediction model was selected from six advanced machine-learning techniques. The receiver operating characteristic (ROC) curves and the area under the curve (AUC) were applied to assess the efficiency of the models. RESULTS: The models with the best performance for pathological invasion prediction and muscular invasion prediction consisted of LASSO as the feature selection method and random forest as the classifier. In the training set, the AUC of the pathological invasion model and muscular invasion model were 0.808 and 0.828. Furthermore, with the mRMR as the feature selection method, the external invasion model based on random forest achieved excellent discrimination (AUC, 0.857). CONCLUSIONS: The full-sequence models demonstrated excellent accuracy for preoperatively predicting the bladder cancer invasion status. CLINICAL RELEVANCE STATEMENT: This study introduces a full-sequence MRI model for preoperative prediction of the depth of bladder cancer infiltration, which could help clinicians to recognise pathological features associated with tumour infiltration prior to invasive procedures. KEY POINTS: • Full-sequence MRI prediction model performed better than Vesicle Imaging-Reporting and Data System (VI-RADS) for preoperatively evaluating the invasion status of bladder cancer. • Machine learning methods can extract information from T1-weighted image (T1WI) sequences and benefit bladder cancer invasion prediction.	bladder
Surgical outcomes of robot-assisted radical cystectomy in octogenarian or older patients: A Japanese nationwide study.	OBJECTIVE: To evaluate the surgical outcomes of robot-assisted radical cystectomy (RARC) in octogenarian or older patients based on a Japanese nationwide database. METHODS: The diagnosis procedure combination database was used to extract the data on radical cystectomy cases. Surgical outcomes of RARC in octogenarian or older patients (older group) were initially compared to those of patients younger than 80 years (younger group). Then, the surgical outcomes of RARC in the older group were compared to those of open radical cystectomy (ORC) and laparoscopic radical cystectomy (LRC) in the same age group. RESULTS: Between 2018 and 2021, 478 RARC cases in the older group and 2257 RARC cases in the younger group were identified. In the older group, ileal conduit, neobladder, and other urinary diversions were carried out in 352 (73.6%), 22 (4.6%), and 104 (21.8%) patients, respectively. In the older group, when compared with the younger group, the complication rate (24.9%), blood transfusion rate (41.4%), and in-hospital mortality (1.4%) were equivalent, while significantly shorter anesthesia time and longer length of stay were observed in the older group (521.0 ± 140.4 min vs. 595.1 ± 141.71 min, p < 0.01, and 32.9 ± 16.8 days vs. 30.6 ± 17.8 days, p = 0.01, respectively). In the comparison of the surgical outcomes of older patients receiving RARC to those receiving ORC (n = 746) and LRC (n = 375), the RARC group had the lowest complication rate and the shortest length of stay, while the shortest anesthesia time was noted in the ORC group. CONCLUSION: The feasibility of RARC for octogenarian or older patients was demonstrated by the nationwide database study.	bladder
Exposure to benzene and other hydrocarbons and risk of bladder cancer among male offshore petroleum workers.	BACKGROUND: Occupational exposures constitute the second leading cause of urinary bladder cancer after tobacco smoking. Increased risks have been found in the petroleum industry, but high-quality exposure data are needed to explain these observations. METHODS: Using a prospective case-cohort design, we analysed 189 bladder cancer cases (1999-2017) and 2065 randomly drawn non-cases from the Norwegian Offshore Petroleum Workers cohort. Cases were identified in the Cancer Registry of Norway, while work histories (1965-1998) and lifestyle factors were recorded by questionnaire at baseline (1998). Occupational petroleum-related hydrocarbon exposures were assessed by expert-developed job-exposure matrices. Hazard ratios were estimated by weighted Cox-regressions, adjusted for age, tobacco smoking, education, and year of first employment, and with lagged exposures. RESULTS: Increased risks were found in benzene-exposed workers, either long-term exposure (≥18.8 years, HR = 1.89, 95% CI: 1.14-3.13; p-trend = 0.044) or high-level cumulative benzene exposure (HR = 1.60, 95% CI: 0.97-2.63; p-trend = 0.065), compared with the unexposed. Associations persisted with 20-year exposure lag. No associations were found with skin or inhalation exposure to crude oil, mineral oil (lubrication, hydraulics, turbines, drilling), or diesel exhaust. CONCLUSIONS: The results suggest that exposures in the benzene fraction of the petroleum stream may be associated with increased bladder cancer risk.	bladder